rs2246477

Positions:

• chr5-172781451-A-G
• chr5-172781451-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650258.1(ENSG00000253736):​n.506-621A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,246 control chromosomes in the GnomAD database, including 1,554 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1554 hom., cov: 32)
• Consequence: ENST00000650258.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377730	XR_941231.2	n.3306-621A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650258.1	n.506-621A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18710 AN: 152128 Hom.: 1551 Cov.: 32

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.00384

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.141

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.123 AC: 18723 AN: 152246 Hom.: 1554 Cov.: 32 AF XY: 0.121 AC XY: 9015 AN XY: 74446

Gnomad4 AFR AF: 0.0346

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.00385

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.138

Alfa AF: 0.138 Hom.: 253

Bravo AF: 0.117

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.84

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2246477; hg19: chr5-172208454;